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@@ -41,25 +41,25 @@ def examineFiles(self,files): |
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# just read the modality type; need to go to reporting logic, since DCMTK
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# is not wrapped ...
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- for file in files:
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+ for cFile in files:
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- uid = slicer.dicomDatabase.fileValue(file, self.tags['instanceUID'])
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+ uid = slicer.dicomDatabase.fileValue(cFile, self.tags['instanceUID'])
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if uid == '':
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return []
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- desc = slicer.dicomDatabase.fileValue(file, self.tags['seriesDescription'])
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- if desc == "":
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- name = "Unknown"
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+ desc = slicer.dicomDatabase.fileValue(cFile, self.tags['seriesDescription'])
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+ if desc == '':
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+ desc = "Unknown"
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- number = slicer.dicomDatabase.fileValue(file, self.tags['seriesNumber'])
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+ number = slicer.dicomDatabase.fileValue(cFile, self.tags['seriesNumber'])
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if number == '':
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number = "Unknown"
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- isDicomSeg = (slicer.dicomDatabase.fileValue(file, self.tags['modality']) == 'SEG')
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+ isDicomSeg = (slicer.dicomDatabase.fileValue(cFile, self.tags['modality']) == 'SEG')
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if isDicomSeg:
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loadable = DICOMLoadable()
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- loadable.files = [file]
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+ loadable.files = [cFile]
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loadable.name = desc + ' - as a DICOM SEG object'
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loadable.tooltip = loadable.name
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loadable.selected = True
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@@ -84,7 +84,7 @@ def referencedSeriesName(self,loadable): |
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return referencedName
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def addReferences(self,loadable):
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- """Puts a list of the referened UID into the loadable for use
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+ """Puts a list of the referenced UID into the loadable for use
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in the node if this is loaded."""
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import dicom
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dcm = dicom.read_file(loadable.files[0])
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@@ -96,7 +96,7 @@ def addReferences(self,loadable): |
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loadable.referencedInstanceUIDs = []
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for f in slicer.dicomDatabase.filesForSeries(dcm.ReferencedSeriesSequence[0].SeriesInstanceUID):
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refDCM = dicom.read_file(f)
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- # this is a hack that should probablybe fixed in Slicer core - not all
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+ # this is a hack that should probably fixed in Slicer core - not all
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# of those instances are truly referenced!
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loadable.referencedInstanceUIDs.append(refDCM.SOPInstanceUID)
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loadable.referencedSeriesUID = dcm.ReferencedSeriesSequence[0].SeriesInstanceUID
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@@ -105,22 +105,17 @@ def load(self,loadable): |
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""" Load the DICOM SEG object
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"""
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print('DICOM SEG load()')
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- labelNodes = vtk.vtkCollection()
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-
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- uid = None
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-
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try:
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uid = loadable.uid
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print ('in load(): uid = ', uid)
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except AttributeError:
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return False
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- res = False
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# make the output directory
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outputDir = os.path.join(slicer.app.temporaryPath,"QIICR","SEG",loadable.uid)
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try:
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os.makedirs(outputDir)
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- except:
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+ except OSError:
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pass
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# produces output label map files, one per segment, and information files with
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@@ -134,7 +129,6 @@ def load(self,loadable): |
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"inputSEGFileName": segFileName,
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"outputDirName": outputDir,
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}
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- seg2nrrd = None
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try:
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seg2nrrd = slicer.modules.seg2nrrd
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except AttributeError:
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@@ -152,7 +146,7 @@ def load(self,loadable): |
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colorLogic = slicer.modules.colors.logic()
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segmentationColorNode = slicer.vtkMRMLColorTableNode()
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segmentationColorNode.SetName(loadable.name)
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- segmentationColorNode.SetTypeToUser();
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+ segmentationColorNode.SetTypeToUser()
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segmentationColorNode.SetHideFromEditors(0)
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segmentationColorNode.SetAttribute("Category", "File")
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segmentationColorNode.NamesInitialisedOff()
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@@ -171,6 +165,7 @@ def load(self,loadable): |
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seriesName = self.referencedSeriesName(loadable)
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segmentNodes = []
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+ labelNode = None
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for segmentId in range(numberOfSegments):
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# load each of the segments' segmentations
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# Initialize color and terminology from .info file
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@@ -266,18 +261,27 @@ def load(self,loadable): |
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# point the label node to the color node we're creating
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labelDisplayNode = labelNode.GetDisplayNode()
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- if labelDisplayNode == None:
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+ if labelDisplayNode is None:
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print ('Warning: no label map display node for segment ',segmentId,', creating!')
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labelNode.CreateDefaultDisplayNodes()
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labelDisplayNode = labelNode.GetDisplayNode()
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labelDisplayNode.SetAndObserveColorNodeID(segmentationColorNode.GetID())
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# TODO: initialize referenced UID (and segment number?) attribute(s)
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+ # dataset = dicom.read_file(segFileName)
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+ # referencedSeries = dict()
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+ # for refSeriesItem in dataset.ReferencedSeriesSequence:
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+ # refSOPInstanceUIDs = []
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+ # for refSOPInstanceItem in refSeriesItem.ReferencedInstanceSequence:
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+ # refSOPInstanceUIDs.append(refSOPInstanceItem.ReferencedSOPInstanceUID)
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+ # referencedSeries[refSeriesItem.SeriesInstanceUID] = refSOPInstanceUIDs
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+ # segmentationNode.SetAttribute("DICOM.referencedInstanceUIDs", str(referencedSeries))
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# create Subject hierarchy nodes for the loaded series
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self.addSeriesInSubjectHierarchy(loadable, labelNode)
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# create a combined (merge) label volume node (only if a segment was created)
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+ mergeNode = None
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if labelNode:
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volumeLogic = slicer.modules.volumes.logic()
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mergeNode = volumeLogic.CloneVolume(labelNode, seriesName + "-label")
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@@ -364,7 +368,7 @@ def examineForExport(self, node): |
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exportable.confidence = 1.0
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exportable.setTag('Modality', 'SEG')
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- if exportable != None:
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+ if exportable is not None:
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exportable.name = self.loadType
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exportable.tooltip = "Create DICOM files from segmentation"
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exportable.nodeID = node.GetID()
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@@ -403,7 +407,7 @@ def exportAsDICOMSEG(self, exportablesCollection): |
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instanceUIDs = subjectHierarchyNode.GetAttribute("DICOM.ReferencedInstanceUIDs").split()
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if instanceUIDs == "":
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- raise Exception("Editor master node does not have DICOM information")
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+ raise Exception("Editor master node does not have DICOM information")
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# get the list of source DICOM files
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inputDICOMImageFileNames = ""
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@@ -423,7 +427,6 @@ def exportAsDICOMSEG(self, exportablesCollection): |
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import vtkSlicerSegmentationsModuleLogic
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logic = vtkSlicerSegmentationsModuleLogic.vtkSlicerSegmentationsModuleLogic()
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- segmentationTransform = vtk.vtkMatrix4x4()
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segmentationNode = subjectHierarchyNode.GetAssociatedNode()
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mergedSegmentationImageData = segmentationNode.GetImageData()
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@@ -489,7 +492,7 @@ def exportAsDICOMSEG(self, exportablesCollection): |
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colorNode.GetColor(labelIndex, rgbColor)
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rgbColor = map(lambda e: e*255., rgbColor)
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- # get the attributes and conver to format CodeValue,CodeMeaning,CodingSchemeDesignator
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+ # get the attributes and convert to format CodeValue,CodeMeaning,CodingSchemeDesignator
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# or empty strings if not defined
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propertyCategoryWithColons = colorLogic.GetSegmentedPropertyCategory(labelIndex, terminologyName)
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if propertyCategoryWithColons == '':
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@@ -525,7 +528,7 @@ def exportAsDICOMSEG(self, exportablesCollection): |
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if anatomicRegion != "":
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attributes += ";AnatomicRegion:" + anatomicRegion
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if anatomicRegionModifier != "":
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- attributes += ";AnatomicRegionModifer:" + anatomicRegionModifier
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+ attributes += ";AnatomicRegionModifier:" + anatomicRegionModifier
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attributes += ";SegmentAlgorithmType:AUTOMATIC"
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attributes += ";SegmentAlgorithmName:SlicerSelfTest"
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attributes += ";RecommendedDisplayRGBValue:%g,%g,%g" % tuple(rgbColor[:-1])
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